## Read 3 sequences from a FASTA file:
ortho <- read.fasta(file = system.file("sequences/ortho.fasta", package =
"seqinr"))
## Select only third codon positions:
ortho3 <- lapply(ortho, function(x) x[seq(from = 3, to = length(x), by = 3)])
## Write the 3 modified sequences to a file:
fname <- tempfile(pattern = "ortho3", tmpdir = tempdir(), fileext = "fasta")
#write.fasta(sequences = ortho3, names = names(ortho3), nbchar = 80, file.out = "ortho3.fasta")
write.fasta(sequences = ortho3, names = names(ortho3), nbchar = 80, file.out = fname)
## Read them again from the same file and check that sequences are preserved:
ortho3bis <- read.fasta(fname, set.attributes = FALSE)
stopifnot(identical(ortho3bis, ortho3))
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